{"id":628,"date":"2017-04-26T15:26:05","date_gmt":"2017-04-26T15:26:05","guid":{"rendered":"https:\/\/wp0.vanderbilt.edu\/rizzolab\/?page_id=628"},"modified":"2017-12-08T16:01:30","modified_gmt":"2017-12-08T16:01:30","slug":"chem-224","status":"publish","type":"page","link":"https:\/\/wp0.vanderbilt.edu\/rizzolab\/chem-224\/","title":{"rendered":"Chem 224"},"content":{"rendered":"\n\n\n
\n
Chem 224<\/b>
\nBioorganic Chemistry<\/b>
\nFall 2014<\/b>
\nT, Th 8:10 – 9:25 AM<\/b>
\nRoom SC 1308, Stevenson Center (SC, Math)<\/a><\/b><\/div>\n<\/td>\n
\n
\n

\u00a0Carmelo Rizzo<\/b>
\noffice: SC 7662<\/b>
\nTel.: 322-6100<\/b>
\ne-mail: c.rizzo@vanderbilt.edu<\/a><\/b><\/p>\n<\/div>\n<\/td>\n<\/tr>\n<\/tbody>\n<\/table>\n

updated: 11\/15\/2014<\/span><\/strong><\/p>\n

Tentative Course Content<\/b><\/p>\n

I. Amino Acids, Peptides, and Proteins<\/p>\n

A. Amino acid structure, properties, chemical synthesis, and analysis<\/p>\n

B. Peptide and Protein: structure, synthesis, and analysis<\/p>\n

C. Combinatorial Libraries<\/p><\/blockquote>\n

II. Enzymes Mechanisms<\/p>\n

A. Catalytic sidechains – proteases, phosphotases<\/p>\n

B. Cofactors<\/p><\/blockquote>\n

III. Nucleosides, Nucleotides and Nucleic Acids<\/p>\n

 <\/p>\n

Prerequisite:<\/b> Chem 220 a and b (Organic Chemistry)<\/p>\n

Text:<\/strong> There is NO<\/i><\/b> required text for this course. Exams and assignments will come entirely from class notes. The bookstore has the following recommended texts:<\/p>\n

\n

Chemical Approaches to the Synthesis of Peptides and Proteins<\/i>, P. Lloyd-Williams, F. Albericio, E. Giralt, CRC Press, Boca Raton,1997. ISBN 0-8493-9142-3<\/p>\n

An Introduction to Enzyme and Coenzyme Chemistry<\/i> (3rd ed),T.D.H. Bugg, Wiley, New York, 2012, ISBN: 1119995949<\/p>\n

Nucleic Acids in Chemistry and Biology <\/i>(3rd ed), G. Michael Blackburn, Michael J. Gait, David Loakes, and David Williams, Royal Society of Chemistry Publishing, 2006, ISBN: 978-0-85404-654-6<\/p><\/blockquote>\n

The following is an excellent review on peptide ligation and combinatorial chemistry and is highly
\nrecommended. You can download a pdf version free of charge from a computer with a Vanderbilt IP
\naddress.<\/p>\n

“Synthesis of Native Proteins by Chemical Ligation<\/a><\/em>” Dawson, P. E.; Kent, S. B. H. Annu. Rev.
\nBiochem.<\/em> 2000<\/strong>, 69<\/em>, 923-960.<\/p>\n

“Synthesis and Applications of Small Molecule Libraries<\/a><\/em>.” Thompson, L. A.; Ellman, J. A. Chem.
\nRev.<\/em> 1996<\/strong>, 96<\/em>, 555-600.<\/p><\/blockquote>\n

The following is an excellent resource on peptide masss spectrometry and is available as an ebook
\nthrough ACORN:<\/p>\n

“Overview of Peptide and Protein Analysis
\nby Mass Spectrometry,”<\/em><\/a> Carr, S. A.; Annan, R. S. Curr Protoc Protein Sci.<\/em> 2001<\/strong> Chapter 16: Unit 16.1.<\/p>\n

“Introduction to Proteomics: Tools for the New Biology<\/em>,” Liebler, D. C., Human Press: 2002<\/p><\/blockquote>\n

Bibliography <\/a><\/p><\/blockquote>\n

Exams:<\/b> Three mid term exams – see class schedule for dates.<\/p>\n

Grading:<\/b> Each exam with count equally toward the final grade. Graduate students are also required to write a short paper (10 page limit) on a topic of their choice (with approval from me), related to bioorganic chemistry. In addition, they will present a short lecture (15 minutes) on their topic. You should choose a topic by Oct. 27.<\/p>\n

Office hours:<\/strong> open – you can stop by anytime you like. It might be best to let me know in advance that you are planning to drop in.<\/p>\n

Questions & Answers Page:<\/span><\/b> I am posting questions and answers from the class, sent to me
\nvia email.<\/span><\/a><\/p>\n

\n

\u00a0\u00a0\u00ca<\/p>\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n
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\u00a0<\/b>Tentative class schedule<\/span><\/b><\/p>\n<\/div>\n<\/td>\n<\/tr>\n

\u00a0Thur., Aug. 21<\/td>\n\u00a0Amino acids: Struture, acid-base chemistry, and chemical synthesis<\/p>\n

The Medical Biochemistry Page<\/a>\u00a0(by Prof. Michael W. King, Univ. of Indiana, School of Medicine)<\/td>\n

\u00a0amino
\nacids<\/a>slides 1-49<\/a><\/b>\u00a0(revised 9\/6\/2012)amino acid acid\/base chemistry problems<\/a><\/td>\n<\/tr>\n
\u00a0Tue., Aug. 26<\/td>\n\u00a0<\/strong>Solid-phase peptide synthesis: Protecting groups, coupling reagents, and the solid support<\/p>\n

\u00a0<\/strong>“Solid-Phase Peptide Synthesis: A Silver Anniversary Repor<\/a>t,” Barany, G.; Kneib-Cordonier, N.; Mullen, D. G. Int. J. Peptide Protein Res.<\/em> 1897<\/strong>, 30<\/strong>, 705-739.<\/p>\n

\u00a0<\/strong>“Chemical Synthesis of Peptides and Proteins<\/a>,” Kent, S.B.H. Ann Rev Biochem.1988<\/strong>, 57<\/em>, 957-989<\/p>\n

\u00a0<\/strong>“Amino Acid-Protecting Group<\/a>,” Isidro-Llobet, A.; Alvarez, M.; Albericio, F. Chem. Rev<\/em>. 2009<\/strong>, 109<\/em>, 2455-2504.<\/td>\n

\u00a0Peptide synthesis problem set<\/a> (answers<\/a>)<\/td>\n<\/tr>\n
Thur., Aug. 28<\/td>\n\u00a0Solid-phase peptide syntheis (con’t):<\/td>\n<\/td>\n<\/tr>\n
Tue., Sept. 2<\/td>\n\u00a0Solid-phase peptide syntheis (con’t): Native peptide ligation; cyclic peptides<\/p>\n

\u00a0<\/strong>“Synthesis of Native Proteins by Chemical Ligation<\/a>” Dawson, P. E.; Kent, S. B. H. Annu. Rev. Biochem. <\/i>2000<\/b>, 69<\/i>, 923-960.<\/p>\n

\u00a0<\/strong>“Contemporary Strategies for Peptide Macrocyclization<\/a>,” White, C. J.; Yudin, A. K. Nature Chem<\/em>. 2011<\/strong>, 3<\/em>, 509-524.<\/td>\n

<\/td>\n<\/tr>\n
\u00a0Thur., Sept. 4<\/td>\n\u00a0Protein Structure: Amino acid analysis and peptide sequencing<\/p>\n

“Introduction to Proteomics: Tools for the New Biology,” Liebler, D. C., Human Press: 2002 available as an ebook through ACORN.<\/p>\n

“Overview of Peptide and Protein Analysis
\nby Mass Spectrometry, ” Carr, S. A.; Annan, R. S. Curr Protoc Protein Sci.<\/em> 2001<\/strong> Chapter 16:Unit 16.1.<\/a><\/p>\n

De Novo Peptide Sequencing Tutorial<\/a><\/td>\n

\u00a0slides 50-84<\/a><\/b>\u00a0(revised 9\/12\/2013)<\/p>\n

Amino Acid Residue Masses<\/a><\/p>\n

Proteomic tools<\/a><\/p>\n

Peptide MS Problems<\/a> (answers<\/a>)<\/td>\n<\/tr>\n

\u00a0Tue., Sept. 9<\/td>\n\u00a0Protein Structure: Methods of protein structure determination<\/td>\n\u00a0slides 85-113<\/a><\/b>\u00a0(revised 9\/12\/2013)<\/td>\n<\/tr>\n
\u00a0Thur., Sept. 11<\/td>\n\u00a0Protein Structure: Hydrogen bonds, the hydrophobic effect, \u03b1-helices, \u03b2-sheets, \u03b2-turns<\/td>\n\u00a0<\/b>Biomolecular Turorial<\/a><\/td>\n<\/tr>\n
\u00a0Tue., Sept. 16<\/td>\n\u00a0Combinatorial Synthesis<\/p>\n

“Synthesis and Applications of Small Molecule Libraries<\/a>.” Thompson, L. A.; Ellman, J. A. Chem. Rev. <\/i>1996<\/b>, 96<\/i>, 555-600.<\/td>\n

\u00a0slides 114-138<\/a><\/b>\u00a0(revised 8\/15\/2013)<\/td>\n<\/tr>\n
\u00a0Thur., Sept. 18<\/td>\n\u00a0Enzyme Chemistry- catalysis, proteases<\/td>\n\u00a0slides 139-187<\/strong><\/a> (revised 9\/24\/2014)<\/td>\n<\/tr>\n
\u00a0Tue., Sept. 23<\/td>\n\u00a0First Hour Exam<\/b><\/td>\n<\/td>\n<\/tr>\n
\u00a0Thur., Sept. 25<\/td>\n\u00a0Enzyme Chemistry- phosphatases<\/td>\n<\/td>\n<\/tr>\n
\u00a0Tue., Sept. 30<\/td>\n\u00a0Cofactor Chemistry- Thiamin and pyridoxal dependent enzymes<\/td>\n\u00a0<\/strong><\/b><\/b><\/td>\n<\/tr>\n
\u00a0<\/em>Thur., Oct. 2<\/td>\n\u00a0Cofactor Chemistry- Pyridoxal dependent enzymes<\/td>\n\u00a0<\/strong><\/b>(mid-semester dificiency report due)<\/td>\n<\/tr>\n
\u00a0Tue., Oct. 7<\/td>\n\u00a0Cofactor Chemistry- Nicotinamide dependent enzymes<\/td>\n\u00a0<\/strong><\/b><\/td>\n<\/tr>\n
\u00a0<\/em>Thur., Oct. 9<\/td>\n\u00a0Cofactor Chemistry- Flavin dependent enzymes<\/td>\n\u00a0slides 188-241<\/strong><\/a> (revised 9\/23\/2013)<\/td>\n<\/tr>\n
\u00a0<\/i>Tue., Oct. 14<\/td>\n\u00a0<\/b>Cofactor Chemistry- Flavin dependent enzymes<\/td>\n<\/td>\n<\/tr>\n
Oct. 16 – 17<\/em><\/td>\n\u00a0October Break- no class<\/i><\/b><\/td>\n\u00a0cofactor mechanism problems<\/a>\u00a0(answers<\/a>)<\/td>\n<\/tr>\n
\u00a0Tue., Oct. 21<\/td>\n\u00a0Cofactor Chemistry- Heme and Vitamin B12 dependent enzymes<\/td>\n<\/td>\n<\/tr>\n
\u00a0<\/i>Thur., Oct. 23<\/td>\n\u00a0Structure and Properties of Nucleosides, Nucleotides and Nucleic Acids (History of DNA<\/a>)<\/p>\n

\u00a0atdbio nucleic acids book<\/a><\/td>\n

\u00a0slides 242-369<\/strong><\/a>\u00a0 <\/strong><\/b>(revised 11\/15\/2014)<\/td>\n<\/tr>\n
\u00a0Tue., Oct. 28<\/td>\n\u00a0Second Hour Exam<\/b><\/td>\n\u00a0Graduate student term paper topics due<\/td>\n<\/tr>\n
\u00a0Thur., Oct. 30<\/td>\n\u00a0DNA Processing Enzymes: DNA polymerases, ligases, restriction endonucleases, PCR, site-directed mutagenesis<\/td>\n\u00a0DNA replication animation <\/a><\/p>\n

Lagging strand synthesis animation<\/a><\/p>\n

PCR animation<\/a><\/td>\n<\/tr>\n

\u00a0Tue., Nov. 4<\/td>\n\u00a0Nucleoside and Solid-phase oligonucleotide synthesis; DNA sequencing<\/td>\n<\/td>\n<\/tr>\n
\u00a0Thur., Nov. 6<\/td>\n\u00a0Nucleotide Biosynthesis<\/td>\n<\/td>\n<\/tr>\n
\u00a0Tue., Nov. 11<\/td>\n\u00a0Nucleoside Analogues as Therapeutic Agents<\/td>\n\u00a0<\/strong><\/b><\/td>\n<\/tr>\n
\u00a0Thur., Nov 13<\/td>\n\u00a0Nucleic Acids as Therapeutic Agents, siRNA<\/td>\n\u00a0RNAi animation<\/a><\/td>\n<\/tr>\n
\u00a0Tue., Nov. 18<\/td>\n\u00a0RNA & Translation; DNA Damage & Repair<\/td>\n\u00a0Transcription animation<\/a><\/p>\n

Translation animation<\/a><\/td>\n<\/tr>\n

\u00a0Thur., Nov. 20<\/td>\n\u00a0Third Hour Exam<\/b><\/td>\n<\/td>\n<\/tr>\n
\u00a0Nov. 22-30<\/em><\/td>\n\u00a0Thanksgiving Break – no classes<\/i><\/b><\/td>\n<\/td>\n<\/tr>\n
\u00a0Tue., Dec. 3<\/td>\n\u00a0Graduate Student Presentations (no class for the undergraduates)<\/td>\n<\/td>\n<\/tr>\n
\u00a0Thur., Dec. 5<\/td>\n\u00a0Graduate Student Presentations (no class for the undergraduates)<\/td>\n\u00a0term papers due for graduate students<\/td>\n<\/tr>\n
<\/td>\n<\/td>\n<\/td>\n<\/tr>\n
<\/td>\n<\/td>\n<\/td>\n<\/tr>\n<\/tbody>\n<\/table>\n<\/div>\n

Exams from Spring 2000:<\/p>\n\n\n\n
\u00a0Exam
\n1<\/a>Answers<\/a><\/td>\n		\u00a0Exam
\n2<\/a>Answers<\/a><\/td>\n		\u00a0Exam
\n3<\/a>Answers<\/a><\/td>\n<\/tr>\n<\/tbody>\n<\/table>\n","protected":false},"excerpt":{"rendered":"

Chem 224 Bioorganic Chemistry Fall 2014 T, Th 8:10 – 9:25 AM Room SC 1308, Stevenson Center (SC, Math) \u00a0Carmelo Rizzo office: SC 7662 Tel.: 322-6100 e-mail: c.rizzo@vanderbilt.edu updated: 11\/15\/2014 Tentative Course Content I. Amino Acids, Peptides, and Proteins A. Amino acid structure, properties, chemical synthesis, and analysis B. Peptide and Protein: structure, synthesis, and…<\/p>\n","protected":false},"author":272,"featured_media":0,"parent":0,"menu_order":0,"comment_status":"closed","ping_status":"closed","template":"page_onecolumn.php","meta":[],"tags":[],"_links":{"self":[{"href":"https:\/\/wp0.vanderbilt.edu\/rizzolab\/wp-json\/wp\/v2\/pages\/628"}],"collection":[{"href":"https:\/\/wp0.vanderbilt.edu\/rizzolab\/wp-json\/wp\/v2\/pages"}],"about":[{"href":"https:\/\/wp0.vanderbilt.edu\/rizzolab\/wp-json\/wp\/v2\/types\/page"}],"author":[{"embeddable":true,"href":"https:\/\/wp0.vanderbilt.edu\/rizzolab\/wp-json\/wp\/v2\/users\/272"}],"replies":[{"embeddable":true,"href":"https:\/\/wp0.vanderbilt.edu\/rizzolab\/wp-json\/wp\/v2\/comments?post=628"}],"version-history":[{"count":8,"href":"https:\/\/wp0.vanderbilt.edu\/rizzolab\/wp-json\/wp\/v2\/pages\/628\/revisions"}],"predecessor-version":[{"id":824,"href":"https:\/\/wp0.vanderbilt.edu\/rizzolab\/wp-json\/wp\/v2\/pages\/628\/revisions\/824"}],"wp:attachment":[{"href":"https:\/\/wp0.vanderbilt.edu\/rizzolab\/wp-json\/wp\/v2\/media?parent=628"}],"wp:term":[{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/wp0.vanderbilt.edu\/rizzolab\/wp-json\/wp\/v2\/tags?post=628"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}